[gmx-users] VMD and trajectory files

[Derrick Guang Yuh Lee]

dear Ilya

thank you for the info, two things though. is there any advantage of
having VMD use the xtc file over the tjr file? and you mentioned the -x
option of mdrun, i'm not a hundred percent sure what you mean by that,
could you please be a bit more detailed about that? thanks.


 - derrick


 derrick Lee
 faculty of Science
 Memorial University of Newfoundland
 k24dgyl at mun.ca or derrickglee at hotmail.com

"a teacher is never a giver of truth - he is a guide, a pointer to the
truth that each student must find for himself. a good teacher is merely a
catalyst."
                                                              - bruce lee

On Thu, 20 Nov 2003, Ilya Chorny wrote:

> VMD can read xtc files as well. VMD reads the corrdinates it doesn't
> need velocities.
>
> Set
>
> nstxtcout = 100
>
> and don't forget the -x option in mdrun
>
> Ilya
>
>
> On Thu, 2003-11-20 at 15:40, Derrick Guang Yuh Lee wrote:
> > dear [gmx-users]
> >
> > i was just curious if someone could help me create a movie for VMD. it had
> > just occured to me that i can use my trajectory file (.tjr) to view my
> > monolayer in VMD, but because it is 1ns simulation, the file is a little
> > too large for VMD and our computers here.
> >
> > so, would anyone be able to inform me of how i could set it up such that
> > my trajectory file prints out the velocities and coordinates of my system
> > about 100 times or so? it'd be appreciated. thanks.
> >
> >
> >  - derrick
> >
> >  derrick Lee
> >  faculty of Science
> >  Memorial University of Newfoundland
> >  k24dgyl at mun.ca or derrickglee at hotmail.com
> >
> > "a teacher is never a giver of truth - he is a guide, a pointer to the
> > truth that each student must find for himself. a good teacher is merely a
> > catalyst."
> >                                                               - bruce lee
> >
> > _______________________________________________
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> --
> ----------------------------------------------------------------
> Ilya Chorny Ph.D.         Department of Pharmaceutical Chemistry
> Postdoctoral Researcher   University of California-San Francisco
> phone: (408)-887-8496     Genentech Hall 600 16th St Box 2240
> fax: (415)502-1411        San Francisco, Ca, 94107
>             email: ichorny at maxwell.ucsf.edu
> ----------------------------------------------------------------
>
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